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AlexandrovLab / SigProfilerExtractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
BSD 2-Clause "Simplified" License
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Only Context working output is 6 and 18 #148

Closed pinunQ closed 2 years ago

pinunQ commented 2 years ago

Hello I am running SigProfilerExtractor command and the only signatures that are received as output are the CH6 and CH18. It does not bring any signature for any number of samples.

Can you please explain the situation happening?

marcos-diazg commented 2 years ago

Dear @pinunQ,

CH is the name given to signatures using a non-standard mutational context (i.e., different from COSMIC standard SBS96, DBS78, ID83 or CN48). Not sure if this is something that can be of interest to your analysis. If you want to use the standard contexts, I recommend you to follow our wiki page instructions at https://osf.io/t6j7u/wiki/home/ and check our video tutorials at https://github.com/AlexandrovLab/SigProfilerExtractor#video_tutorials.

I hope this helps, and please feel free to reopen the ticket if you have further questions.